Stark and Sil were inside the ship flying through space. He was originally a little worried about being blasted or shot at while trying to escape. The black pods were used as they had more success landing on the planets than the ships.
However, for some reason they were safe as they went toward the planet. This was all because Logan was causing chaos inside with the androids. They didn't even have time to focus on the ship and had no idea who was on board.
If they did, if Jack knew, then certainly they would have put all of their fire power towards destroying the ship.
Heading back, they were heading to one of the three frontal planets that had been attacked, and the planet of choice was where Wince currently was at. This is what they had agreed.
They needed help, and with the power of Sil they would be able to defeat whatever enemies came their way, hopefully with the humans on their side. Yet, it didn't work out like that.
